Genomics of Indian SARS-CoV-2: Implications in genetic diversity, possible origin and spread of virus

Mondal, Mainak; Lawarde, Ankita; Somasundaram, Kumaravel

doi:10.1101/2020.04.25.20079475

Cited by 17 publications

(22 citation statements)

References 15 publications

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“…This preprint showed the role of NSP1 in translational shutdown and innate immune evasion). Understanding the genetic diversity of a viral gene is key in understanding evolutionary pressure and add one more dimension to virtual screening (Kasibhatla et al 2020;Somasundaram et al 2020). NSP1 is evolving with key residues being conserved.…”

Section: Discussionmentioning

confidence: 99%

Computational search for potential COVID-19 drugs from FDA-approved drugs and small molecules of natural origin identifies several anti-virals and plant products

2020

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The world is currently facing the COVID-19 pandemic, for which mild symptoms include fever and dry cough. In severe cases, it could lead to pneumonia and ultimately death in some instances. Moreover, the causative pathogen is highly contagious and there are no drugs or vaccines for it yet. The pathogen, SARS-CoV-2, is one of the human coronaviruses which was identified to infect humans first in December 2019. SARS-CoV-2 shares evolutionary relationship to other highly pathogenic viruses such as Severe Acute Respiratory Syndrome (SARS) and Middle East respiratory syndrome (MERS). We have exploited this similarity to model a target non-structural protein, NSP1, since it is implicated in the regulation of host gene expression by the virus and hijacking of host machinery. We next interrogated the capacity to repurpose around 2300 FDA-approved drugs and more than 3,00,000 small molecules of natural origin towards drug identification through virtual screening and molecular dynamics. Interestingly, we observed simple molecules like lactose, previously known anti-virals and few secondary metabolites of plants as promising hits. These herbal plants are already practiced in Ayurveda over centuries to treat respiratory problems and inflammation. Disclaimer: we would not like to recommend uptake of these small molecules for suspect COVID patients until it is approved by competent national or international authorities.

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Section: Discussionmentioning

confidence: 99%

Computational search for potential COVID-19 drugs from FDA-approved drugs and small molecules of natural origin identifies several anti-virals and plant products

2020

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“…During the preparation of this manuscript, we realized that some of the variants are also the topic of other papers and preprints predating this work e.g. (Korber et al 2020;Banerjee et al 2020;Somasundaram, Mondal, and Lawarde 2020;Begum et al 2020;Bai et al 2020;Yang et al 2020;Pachetti et al 2020). The fact that we identify some of the previously known mutations by using a different approach indicates that they represent a genuine signal rather than artefacts; however, this does not necessarily mean that their increase in time (see below) is a consequence of a correspondingly increased transmissibility rate or aggressiveness in general -for which at the moment there is no conclusive data as stated in most of the available preprints.…”

Section: Position 84 In Orf8mentioning

confidence: 99%

Insurgence and worldwide diffusion of genomic variants in SARS-CoV-2 genomes

Comandatore

Chiodi

Gabrieli

et al. 2020

Preprint

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The SARS-CoV-2 pandemic that we are currently experiencing is exerting a massive toll both in human lives and economic impact. One of the challenges we must face is to try to understand if and how different variants of the virus emerge and change their frequency in time. Such information can be extremely valuable as it may indicate shifts in aggressiveness, and it could provide useful information to trace the spread of the virus in the population. In this work we identified and traced over time 7 amino acid variants that are present with high frequency in Italy and Europe, but that were absent or present at very low frequencies during the first stages of the epidemic in China and the initial reports in Europe. The analysis of these variants helps defining 6 phylogenetic clades that are currently spreading throughout the world with changes in frequency that are sometimes very fast and dramatic. In the absence of conclusive data at the time of writing, we discuss whether the spread of the variants may be due to a prominent founder effect or if it indicates an adaptive advantage.

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“…The patient had traveled from Wuhan, China [12,13] . The initial genomic identity of the virus was also established which mapped to the B superclade of SARS-CoV-2 [14] . Further introductions into the state during the later days of the pandemic through international and regional travel could have contributed to the spread of the epidemic in the state and the pool of circulating genetic lineages or clades.…”

Section: Introductionmentioning

confidence: 99%

“…Further introductions into the state during the later days of the pandemic through international and regional travel could have contributed to the spread of the epidemic in the state and the pool of circulating genetic lineages or clades. While a number of studies on the genetic epidemiology of SARS-CoV-2 from different states in India have emerged [14][15][16][17] , there has been a paucity of information on the genetic architecture and epidemiology of SARS-CoV-2 isolates in the state of Kerala.…”

Section: Introductionmentioning

confidence: 99%

Initial insights into the genetic epidemiology of SARS-CoV-2 isolates from Kerala suggest local spread from limited introductions

Radhakrishnan

Divakar

Jain

et al. 2020

Preprint

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Coronavirus disease 2019 (COVID-19) rapidly spread from a city in China to almost every country in the world, affecting millions of individuals. Genomic approaches have been extensively used to understand the evolution and epidemiology of SARS-CoV-2 across the world. Kerala is a unique state in India well connected with the rest of the world through a large number of expatriates, trade, and tourism. The first case of COVID-19 in India was reported in Kerala in January 2020, during the initial days of the pandemic. The rapid increase in the COVID-19 cases in the state of Kerala has necessitated the understanding of the genetic epidemiology of circulating virus, evolution, and mutations in SARS-CoV-2. We sequenced a total of 200 samples from patients at a tertiary hospital in Kerala using COVIDSeq protocol at a mean coverage of 7,755X. The analysis identified 166 unique high-quality variants encompassing 4 novel variants and 89 new variants identified for the first time in SARS-CoV-2 samples isolated from India. Phylogenetic and haplotype analysis revealed that the circulating population of the virus was dominated (94.6% of genomes) by three distinct introductions followed by local spread, apart from identifying polytomies suggesting recent outbreaks. The genomes formed a monophyletic distribution exclusively mapping to the A2a clade. Further analysis of the functional variants revealed two variants in the S gene of the virus reportedly associated with increased infectivity and 5 variants that mapped to five primer/probe binding sites that could potentially compromise the efficacy of RT-PCR detection. To the best of our knowledge, this is the first and most comprehensive report of genetic epidemiology and evolution of SARS-CoV-2 isolates from Kerala.

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Genomics of Indian SARS-CoV-2: Implications in genetic diversity, possible origin and spread of virus

Cited by 17 publications

References 15 publications

Computational search for potential COVID-19 drugs from FDA-approved drugs and small molecules of natural origin identifies several anti-virals and plant products

Computational search for potential COVID-19 drugs from FDA-approved drugs and small molecules of natural origin identifies several anti-virals and plant products

Insurgence and worldwide diffusion of genomic variants in SARS-CoV-2 genomes

Initial insights into the genetic epidemiology of SARS-CoV-2 isolates from Kerala suggest local spread from limited introductions

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